Since the game is all about storm chasing, then imo I'd rather have the clouds cause the FPS problem instead of say the player models, or even the landscape (wierd preference, I know).

Ive tried to do a much simpler code with moving clouds, and from that result you can get either

1. AWSOME looking clouds, horrible framerate. With these clouds using several sprites to comprise the clouds.

or

2. HORRIBLE looking clouds, awsome framerate

The only problem you have is something that is generally a problem altogether, and thats lots of transparent sprites in front and behind each other (overdraw).